What if Elizabeth had come back? What if Samantha had stayed? What if John had been sleeping with both of them? John/Elizabeth. John/Samantha with eventual John/Elizabeth/Samantha. Doesn't have to be NC17 though if so it might just be the first for that particular threesome.
10,000 years is a long time to be alone, and to be alone like that can drive a person or city to insanity. This is where Atlantis is not just a city. Her time alone drove her into insanity and when the expidition arrives she takes the ones with the gene along with her. It can either be gradual or all at once but gene or not Mckay must be driven insane with the carriers. He and Sheppard are the cities 'favorites'. It can McShep. Bonus points to whoever can make it mostly cannon up until the ancients try to kick the expidition from Atlantis.